The children's anime revolves around Velonica, a high-handed and ultra-selfish little alien girl on the Galaxy Network, who begins to cause havoc on Earth. After a "fated encounter" with an Earthling boy, Velonica wavers between a possible budding romance with the boy and her dedication to the arts.

A psychic ninja fantasy suggesting that the assassins did not die out during the Sengoku era but burrowed under Japan, where they fought a new war against the alien occupants of a crashed spaceship that has lain undisturbed for several millennia.

The young girl Clara visits her Aunt Gerda and Uncle Drosselmeyer. Her aunt tells her scary stories about the Ragman, a creepy and mysterious man who turns children into mice if they don't go to bed on time. The Ragman is always spying on sleeping children searching for more victims. Just before Clara goes to bed her eccentric uncle gives her a wooden nutcracker doll. He's a bit embarrassed because the only part on the doll that's perfect is the heart, but Clara loves her new doll. She falls asleep but wakes up hearing mice squeaking...

To commemorate the anime Flying Witch, the first volume of the Blu-ray/DVD release included a special episode of Flying Witch Petit.